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(Add Thredds catalogs and crontab and install packages)
Line 21: Line 21:
 
  > su
 
  > su
 
  > yum update
 
  > yum update
 
  
 
===Configure users and groups===
 
===Configure users and groups===
Line 145: Line 144:
  
 
===Add Thredds catalogs and crontab and install packages===
 
===Add Thredds catalogs and crontab and install packages===
These steps were not in Xen OpenDAP configuration - Guillaume made them and it was hard to detail the steps.
 
 
*Pass the catalogs from the Xen OpenDAP to VMWare OpenDAP
 
*Pass the catalogs from the Xen OpenDAP to VMWare OpenDAP
# In the Xen VM, started a htppd service, copied Thredds catalogs to shared folder under /catalogs and changed permissions for user apache so that in browser opendap.mohid.com/catalogs it was possible to see the catalogs files listed.
+
# In the Xen VM, create a new folder /opendap/catalogs and copy the catalogs from apache folder/content/threadds
# In the VMWare VM each file was downloaded to /home/user/Downloads/apache-tomcat-7.0.23/content/threadds (and rewrited).
+
# In the VMWare VM copy the files (visible in network) to /home/user/Downloads/apache-tomcat-7.0.23/content/threadds (and rewrited).
 
# Each catalog was open in vim to replace each appearence of tomcat folder (versions were different)
 
# Each catalog was open in vim to replace each appearence of tomcat folder (versions were different)
  
 
*Pass the crontab from the Xen OpenDAP to VMWare OpenDAP
 
*Pass the crontab from the Xen OpenDAP to VMWare OpenDAP
# In the Xen OpenDAP it was saved the crontab as txt file to be seen in opendap.mohid.com as previously.
+
# In the Xen OpenDAP copy the crontab and save as txt file to be shared as previously.
 
# In the VMWare the text file was saved to /home/user/Downloads
 
# In the VMWare the text file was saved to /home/user/Downloads
  
*Install necessary packages
+
*Install necessary packages so that the Thredds (and scripts) work:
 
Install Netcdf, nco and ruby
 
Install Netcdf, nco and ruby
 
  > yum install netcdf
 
  > yum install netcdf
Line 178: Line 176:
 
*In Samba Server Configuration tool (Application->Other->Samba) edited workgroup as MARETEC, users datamover and added /opendap folder share (acces to datamover)
 
*In Samba Server Configuration tool (Application->Other->Samba) edited workgroup as MARETEC, users datamover and added /opendap folder share (acces to datamover)
  
===Change LVM===
 
*First reduce /home size from 50GB to 10GB
 
>su
 
>init 3                                            (boot-nogui)
 
 
>fuser -m /home
 
/home    1122m
 
>ps auxw | grep 1222
 
apache-tomcat...
 
>service tomcat stop
 
>umount /home
 
>resize2fs -p /dev/vg_opendap2/lv_home 10G
 
>e2fsck -f /dev/vg_opendap2/lv_home                (required before resize)
 
>resize2fs -p /dev/vg_opendap2/lv_home 10G
 
>lvm lvresize /dev/vg_opendap2/lv_home --size 10G
 
 
*In the future do the same for root from 50GB to 30GB
 
Boot with rescue cd - esc while booting to select in boot menu the cd with the installation and then select rescue fedora. When system message appears "The rescue environment will now attempt to find your Linux installation and mount it under the directory /mnt/sysimage." click skip and goes to command prompt
 
bash-4.2>lvm vgchange -a y
 
bash-4.2>umount /root
 
bash-4.2>resize2fs -p /dev/vg_opendap2/lv_root 20G
 
bash-4.2>e2fsck -f /dev/vg_opendap2/lv_root                (required before resize)
 
bash-4.2>resize2fs -p /dev/vg_opendap2/lv_root 20G
 
bash-4.2>lvm lvresize /dev/vg_opendap2/lv_root --size 20G
 
 
*Resize PV to the new available volume (300GB) and create a new LV (opendap) 270GB
 
Can't change vg size (only remove disks from it with vgreduce) so it has to reduce/increase the physical volume associated (it is better to have only one physical volume because there is only one disk, so enlarge physical volume)
 
Still in rescue fedora
 
bash-4.2>lvm pvs
 
PV        VG          Fmt  Attr PSize  PFree
 
  /dev/sda3 vg_opendap2 lvm2 a-  99.50G 67.30G
 
bash-4.2>lvm pvresize /dev/sda3 --setphysicalvolumesize 300G
 
need to delete and create lv_swap to move it from the end of the PV to the beggining. or it does not allow to do the pvresize
 
bash-4.2>lvm lvs            (to know the size of swap to create a new with the same size
 
LV        VG
 
..
 
lv_swap  vg_opendap2  -wi-a-  1.97g
 
bash-4.2>lvm lvremove /dev/vg_opendap2/lv_swap
 
bash-4.2>lvm lvcreate --size 1.97G --name lv_swap vg_opendap2
 
bash-4.2>mkswap /dev/vg_opendap2/lv_swap
 
bash-4.2>lvm pvresize /dev/sda3 --setphysicalvolumesize 300G
 
bash-4.2>lvm pvs
 
PV        VG          Fmt  Attr PSize  PFree
 
  /dev/sda3 vg_opendap2 lvm2 a-  299.97G 267.97G
 
bash-4.2> lvcreate -n opendap -L 260G vg_opendap2
 
 
THIS STEP PROBABLY CRASHED THE MACHINE
 
  
 
===Future tasks===
 
===Future tasks===

Revision as of 18:10, 10 January 2012

Create VM in VMWare vSphere

1GB RAM
300GB. 
Linux Red Hat FEDORA 16. FEDORA 10 (Xen OpenDAP version) was not accesible
1 CPU
Installed VMTools from the console making a CD Link to the VMWareTools in \\Davinci\Software\VMWare\Tools. vSphere does not support the linux version to do the installation from vSphere.

Configure VM in FEDORA console

This steps were made based on Xen OpenDAP configuration wiki and with help from Guillaume.

During installation chose a custom partition definition.

Created partition 'sda1' - boot (2MB) and partition 'sda2' - PV (300GB). 
created VG 'vg_opendap2' and 
i) LV 'swap' (swap fs 2GB); 
ii) LV 'root' (ext4 fs) in / (30GB)
iii) LV 'home' (ext4 fs) in /home (10GB)
iv) LV 'opendap' (ext4 fs) in /opendap (265GB)

Update your distro

> su
> yum update

Configure users and groups

  • Go to Other-->Users and groups
  • Make users the primary group of user user.
  • Create the group Maretec. Every user of this system should be applied to the group Maretec.
  • Create the user datamover. Make his primary group Maretec.

Configure permissions

> chgrp -R maretec /opendap 
> chmod g+w /opendap

Configure the firewall

From the X environment, open up the Applications-->Other-->Firewall. Then open up the ports 22(ssh), and 8080(tomcat) (add).

Enable sshd

> vim /etc/ssh/sshd_config
sshd_config> #PermitRootLogin yes
sshd_config> PermitRootLogin no
Remeber in vim:
i - insert
:w - save
:q - quit
> service sshd start
> service sshd status
> chkconfig --level 345 sshd on
> chkconfig | grep sshd

Install Thredds

It is needed java and apache tomcat.

  • Download current Java SE Developer Kit (JDK) from Sun for linux (.tar.gz file)
  • extract the zip file in the current folder or copy it to the destination folder before this command as a regular user (not as root).
> cd [destinationfolder]                   'in this case [destinationfolder] was /home/user/Downloads/
> tar xvzf [tarfilename]                   'in this case [tarfilename] was jdk-7u2-linux-i586.tar.gz
  • Download apache tomcat for linux (.tar.gz file)
  • extract the zip file in the current folder or copy it to the destination folder before this command as a regular user (not as root).
> cd [destinationfolder]                   'in this case [destinationfolder] was /home/user/Downloads/
> tar xvzf [tarfilename]                   'in this case [tarfilename] was apache-tomcat-7.0.23.tar.gz
  • start the apache,
> cd [apachefolder]                        'in this case [apachefolder] was /home/user/Downloads/apache-tomcat-7.0.23
> bin/startup.sh
  • and check that responds.
test nº1:
> ps -ef | grep tomcat

and test nº2: 
Open a new browser window/tab and go to http://localhost:8080/ to verify Tomcat is running a message appers saying that 
"If you're seeing this page trough a web page it means that you have setup tomcat sucessfull"
  • Download the TDS WAR file from Unidata's web site.
  • copy the thredds.war file to the apache /webapps folder
> cp [folderorigin]/thredds.war [apachefolder]/webapps     'in this case [apachefolder] was /home/user/Downloads/apache-tomcat-7.0.23 and [folderorigin] was /home/user/Downloads
  • Assure that tomcat is launched at startup:

These steps were different than in Xen OpenDAP configuration because it did not worked - Guillaume made them. 1) Create a script saved in /etc/init.d/tomcat as root

> su
> touch /etc/init.d/tomcat             'creates an empty file
> chmod a+rx /etc/init.d/tomcat        'permissions(+) reading and executing (r e x) for all (a)
> vim /etc/init.d/tomcat

tomcat>
#! /bin/sh
#
# tomcat:       Starts the tomcat Daemon
#
# chkconfig: 345 96 02
# processname: apache-tomcat
# description: tomcat fedora init script \
# config:
# Author: Brito e Riflet

base=${0##*/}

# See how we were called.
case "$1" in
 start)
       /home/user/Downloads/apache-tomcat-7.0.23/bin/startup.sh
       RETVAL=0
       ;;
 stop)
       /home/user/Downloads/apache-tomcat-7.0.23/bin/shutdown.sh
       RETVAL=0
       ;;
 restart)
       /home/user/Downloads/apache-tomcat-7.0.23/bin/shutdown.sh
       echo "Waiting for daemon to exit..."
       sleep 5
       /home/user/Downloads/apache-tomcat-7.0.23/bin/startup.sh
       RETVAL=0
       ;;
 *)
       echo $"Usage: $0 {start|stop|restart}"
       exit 2
       ;;
esac

exit $RETVAL
>chmod a+rwx -R /home

2) Create a link to the script

> cd /etc/rc.d/rc3.d                         'tomcat initialization in init level 3
> ln -s ../init.d/tomcat S30tomcat           'symbolic link for the script in init.d/tomcat
> exit

3) Test the script and connectivity

> service tomcat start                       'Test the script
> service tomcat stop
> service tomcat restart
> netstat -tlnap | grep 8080                 'Test if 8080 port is activ (tomcat port)

4) Test if tomcat service is started in boot Restart the VM and test http://localhost:8080 in web browser. it should say

"If you're seeing this page trough a web page it means that you have setup tomcat sucessfull"

Add Thredds catalogs and crontab and install packages

  • Pass the catalogs from the Xen OpenDAP to VMWare OpenDAP
  1. In the Xen VM, create a new folder /opendap/catalogs and copy the catalogs from apache folder/content/threadds
  2. In the VMWare VM copy the files (visible in network) to /home/user/Downloads/apache-tomcat-7.0.23/content/threadds (and rewrited).
  3. Each catalog was open in vim to replace each appearence of tomcat folder (versions were different)
  • Pass the crontab from the Xen OpenDAP to VMWare OpenDAP
  1. In the Xen OpenDAP copy the crontab and save as txt file to be shared as previously.
  2. In the VMWare the text file was saved to /home/user/Downloads
  • Install necessary packages so that the Thredds (and scripts) work:

Install Netcdf, nco and ruby

> yum install netcdf
> yum install nco
> yum install ruby

Make the machine folders visible with Samba

> yum install samba
> service smb start
> chkconfig --level 345 smb on
> chkconfig | grep smd
> smbpasswd -a datamover                                  (Typed the datamover Password)
> vim /etc/samba/smb.conf
smb.conf> see a typical config here         (did not changed nothing here, used Samba server configuration tool, below)
> chcon -R -t samba_share_t /opendap                      (change file SELinux security context to folder opendap)
  • Change permissions in folder /opendap:
> chmod a+rwx -R /opendap         'to all (a) give permissions (+) read (r), write (w) and execute (x)
  • In Firewall allowed samba and samba client as trusted
  • Installed Samba Server Configuration tool
> su
> yum install system-config-samba
  • In Samba Server Configuration tool (Application->Other->Samba) edited workgroup as MARETEC, users datamover and added /opendap folder share (acces to datamover)


Future tasks

  • Copy all the content from Xen Opendap to new Opendap2.
  • Change crontab. Use the text file saved in Downloads to copy the content to crontab:
>crontab -e                 'edit crontab


Links

Go Back to VMWare

Xen OpenDAPserver